ArticleNucleic acids research2002
MODBASE, a database of annotated comparative protein structure models.
Article in Nucleic acids research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
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- Structural insights into a novel interkingdom signaling circuit by cartography of the ligand-binding sites of the homologous quorum sensing LuxR-family.International journal of molecular sciences · 2013Article
- Biodegradation of single-walled carbon nanotubes by eosinophil peroxidase.Small (Weinheim an der Bergstrasse, Germany) · 2013Article
- Comprehensive database of Chorismate synthase enzyme from shikimate pathway in pathogenic bacteria.BMC pharmacology & toxicology · 2013Article
- False discovery rate estimation for cross-linked peptides identified by mass spectrometry.Nature methods · 2012Article
- PSS-3D1D: an improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences.Journal of structural and functional genomics · 2011Article
- Function of human Rh based on structure of RhCG at 2.1 A.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- SKPDB: a structural database of shikimate pathway enzymes.BMC bioinformatics · 2010Article
- Exploring CYP1A1 as anticancer target: homology modeling and in silico inhibitor design.Journal of molecular modeling · 2008Article
- Improving the accuracy of protein secondary structure prediction using structural alignment.BMC bioinformatics · 2006Article
- Advances in homology protein structure modeling.Current protein & peptide science · 2006Review
- MODBASE: a database of annotated comparative protein structure models and associated resources.Nucleic acids research · 2006Article
- Virtual screening of chemical libraries.Nature · 2004Review
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5 authors.
Funding
Abstract
MODBASE (http://guitar.rockefeller.edu/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on PSI-BLAST, IMPALA and MODELLER. MODBASE uses the MySQL relational database management system for flexible and efficient querying, and the MODVIEW Netscape plugin for viewing and manipulating multiple sequences and structures. It is updated regularly to reflect the growth of the protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different datasets. The largest dataset contains models for domains in 304 517 out of 539 171 unique protein sequences in the complete TrEMBL database (23 March 2001); only models based on significant alignments (PSI-BLAST E-value < 10(-4)) and models assessed to have the correct fold are included. Other datasets include models for target selection and structure-based annotation by the New York Structural Genomics Research Consortium, models for prediction of genes in the Drosophila melanogaster genome, models for structure determination of several ribosomal particles and models calculated by the MODWEB comparative modeling web server.
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